Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DsuzGB1 Primary Table: RepeatModeler_DNA Data last updated: 2014-11-20
Big Bed File: /gbdb/DsuzGB1/bbi/DsuzGB1_DNA.bb
Item Count: 15,799
Format description: RepeatMasker .out record

field	example	description
`chrom`	AWUT01012676	Genomic sequence name
`chromStart`	25669	Start in genomic sequence
`chromEnd`	25912	End in genomic sequence
`name`	rnd-5_family-707	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	1614	Smith Waterman alignment score
`milliDiv`	14.5	Base mismatches in parts per thousand
`milliDel`	2.3	Bases deleted in parts per thousand
`milliIns`	1.3	Bases inserted in parts per thousand
`genoLeft`	-68683	-#bases after match in genomic sequence
`repClass`	DNA	Class of repeat
`repFamily`	TcMar-Mariner	Family of repeat
`repStart`	0	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	980	End in repeat sequence
`repLeft`	735	-#bases after match (if strand is +) or start (if strand is -) in repeat sequence

Sample Rows

chrom	chromStart	chromEnd	name	strand	swScore	milliDiv	milliDel	milliIns	genoLeft	repClass	repFamily	repStart	repEnd	repLeft
AWUT01012676	25669	25912	rnd-5_family-707	-	1614	14.5	2.3	1.3	-68683	DNA	TcMar-Mariner	0	980	735
AWUT01012676	25912	25982	rnd-1_family-862	+	597	1.4	0.0	0.0	-68613	DNA	TcMar-Mariner	1	70	0
AWUT01012676	25996	26077	rnd-5_family-707	-	405	11.7	1.2	5.1	-68518	DNA	TcMar-Mariner	-434	546	469
AWUT01012676	26061	26119	rnd-6_family-113	-	375	10.3	0.0	0.0	-68476	DNA	TcMar-Mariner	-10	71	14
AWUT01012676	26131	26301	rnd-1_family-582	-	897	12.7	1.2	3.0	-68294	DNA	TcMar-Mariner	-9	167	1
AWUT01012676	26323	26379	rnd-1_family-838	-	415	7.1	0.0	0.0	-68216	DNA	TcMar-Mariner	0	56	1
AWUT01012676	26430	26555	rnd-5_family-707	-	816	9.7	0.0	0.8	-68040	DNA	TcMar-Mariner	-781	199	76
AWUT01012676	28623	28749	rnd-1_family-497	+	884	9.5	0.0	0.0	-65846	DNA	PIF-Harbinger	14	139	-2
AWUT01012676	32861	33325	rnd-1_family-242	+	2470	5.0	9.2	0.0	-61270	DNA	MITE	2	510	0
AWUT01012676	33699	34260	rnd-1_family-576	-	4174	3.9	0.3	0.9	-60335	DNA	TcMar-Mariner	0	553	110

RepeatModeler (RepeatModeler) Track Description


	Description This track shows the transposon fragments identified by RepeatMasker using the species-specific RepeatModeler library constructed by the GEP. The consensus sequences produced by RepeatModeler were reclassified using the protocol described in the supplemental methods section. References Smit, AFA, Hubley, R. RepeatModeler Open-1.0. http://www.repeatmasker.org. 2008-2010. Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.

Description

References